Unai Emery’s side continued their turnaround in form after a slow start to the campaign and picked up a fourth straight win across all competitions, and their first league victory at home this season.
Man City do not enjoy visiting Villa Park and have now lost their last four league games there, while Enzo Maresca saw his 100 per cent league start as City boss vanish.
Another tough afternoon in the west Midlands started when Marc Guehi’s mistake allowed Jackson to give Villa an early lead.
Villa had keeper Zion Suzuki to thank for making several vital saves, and Iliman Ndiaye crashed an effort off the post as Villa held strong to take the lead into the break.
Erling Haaland grabbed his ninth league goal of the season to get City level but Jackson buried his second of the afternoon – his fourth of the season – on the hour mark to hand Villa the points.
The visitors were greeted with more boos from an away ground ahead of kick-off after they were found guilty of serious breaches of the competition’s financial regulations last month.
City conceded a corner after Gianluigi Donnarumma took too long to take his goal-kick which put City on the back foot, and Villa’s quick start was rewarded with the opener in the sixth minute.
Guehi was unable to control the ball and he instead spilled it into the path of John McGinn, who played it into Jackson and he expertly finished into the top of the net.
The early goal did not dent City’s confidence, and they were denied an equaliser when Suzuki sprung right to push Ndiaye’s curling effort away.
The Japan goalkeeper was getting busier by the minute, he put out an outstretched arm to thwart Rayan Cherki following some neat footwork by Jeremy Doku before stopping Abdukodir Khusanov from range.
Ndiaye had already threatened Suzuki once by cutting inside and letting one rip, and he did it again, only to see the effort slam off the outside of the post.
Haaland had a quiet first half but made his contribution seven minutes after the break to get City level when he nodded Ndiaye’s cross past Suzuki.
City’s onslaught continued and Villa’s woodwork was rattled again, this time Suzuki tipped Josko Gvardiol’s ferocious strike off the bar.
And that save proved decisive as Villa retook the lead just as it looked like City were turning up the heat on the hour mark.
Villa turned defence into attack with precision. Victor Lindelof’s ball set them on the front foot and it ended up with substitute Ibrahim Mbaye, and his first major contribution was to tee up Jackson who saw his strike squeeze past Donnarumma.
City threw everything at getting an equaliser, and Haaland thought he nodded City level for a second time but his goalbound header was blocked by Ian Maatsen as Villa took the points.